The road is full of flowers.
Nature awarded you with these prize
Walking to see butterflies…
Free my mind from a tight cubicle
Of dim light & room full of papers,
Block my mind, blur my sight, freeze my hand.
Let’s make plan, see flowers, worth the time.
We are in the era with 100,000 protein structures available. Now we need to analyse what the crystallographic community already have rather than predicting probes in the vacuum.
When you know the ligand is bound inside the identifiable PDB crystal structure, it is surely affect that protein and we showed you the associated Ki from peer-review literature. So that is how we build the bridge from structures to precision medicine.
The residues that you want to fish out from the multiple alignment conservation may be there but may not be a must. The atoms that must be there are atoms that stay there and pair up with the ligand most of the time. The residues that causes the change in binding affinities is what you want to fish for selectivity.
What the drug community need is perhaps a linker such as MANORAA to go all the way from ligands to proteins, pathways, SNPs and target human organs plus a bit of help from the collaborative effort from various disciplines.
It is the very first attempt that ligand structures can complement the drug discovery pipeline with mostly experimental data source support to the expression levels.
It works on your phone, tablet, mac and PC so I can browse my drug on the go.
Its ligand superposition function allows you to make programmable code for fragments superposition on the URL so your drug fragment remains anonymous.
It is open and free but we will need to survive on citation.